Blender resets restricted rendering settings upon frame change
I have been able to come up with a workaround for both my questions.
It is possible to remove desired particle species for all frames of the render by setting their radius ('scale factor') to 0 in the 'Molecule' section of the Cellblender add-on. They will therefore still be turned on for the render, but invisible due to zero volume.

This enables to not just render one or multiple images, but also an whole animation. Then it is possible to extract all single frames of that animation either from the temporary directory by hand or by choosing 'save all images' of the render window.